@@ -2,5 +2,5 @@

 R/.DS_Store

 vignettes/.DS_Store

 *~

-*.Rhistrory

+*.Rhistory

 .svn

@@ -1 +1,4 @@

 .git

+.Rhistory

+R/.Rhistory

+

@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.3.8

+Version: 1.3.10

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -13,6 +13,7 @@ S3method(fortify,nhx)

 S3method(fortify,obkData)

 S3method(fortify,paml_rst)

 S3method(fortify,phangorn)

+S3method(fortify,phylip)

 S3method(fortify,phylo)

 S3method(fortify,phylo4)

 S3method(fortify,r8s)

@@ -84,6 +85,7 @@ export(read.hyphy)

 export(read.jplace)

 export(read.nhx)

 export(read.paml_rst)

+export(read.phylip)

 export(read.r8s)

 export(read.raxml)

 export(read.tree)

@@ -110,6 +112,7 @@ exportClasses(jplace)

 exportClasses(nhx)

 exportClasses(paml_rst)

 exportClasses(phangorn)

+exportClasses(phylip)

 exportClasses(r8s)

 exportClasses(raxml)

 exportMethods(get.fields)

@@ -126,6 +129,7 @@ exportMethods(plot)

 exportMethods(reroot)

 exportMethods(scale_color)

 exportMethods(show)

+importFrom(Biostrings,BStringSet)

 importFrom(Biostrings,DNAStringSet)

 importFrom(Biostrings,GENETIC_CODE)

 importFrom(Biostrings,readBStringSet)

@@ -174,6 +178,7 @@ importFrom(ggplot2,ggplotGrob)

 importFrom(ggplot2,ggproto)

 importFrom(ggplot2,guide_legend)

 importFrom(ggplot2,guides)

+importFrom(ggplot2,last_plot)

 importFrom(ggplot2,layer)

 importFrom(ggplot2,position_nudge)

 importFrom(ggplot2,scale_color_manual)

@@ -1,5 +1,10 @@

+CHANGES IN VERSION 1.3.10

+------------------------

+ o support phylip tree format and update vignette of phylip example <2016-01-15, Fri>

+

 CHANGES IN VERSION 1.3.9

 ------------------------

+ o optimize getYcoord <2016-01-14, Thu>

  o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>

  o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.

    these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>

@@ -3,98 +3,23 @@ setOldClass("multiPhylo")

 setOldClass("gg")

 setOldClass("ggplot")

-supported_tree_object <- function() {

-    c("hyphy", "r8s", "nhx", "apeBootstrap", "raxml",

-      "paml_rst", "phangorn", "codeml_mlc", "codeml",

-      "jplace", "beast")

-}

+setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))

-##' Class "hyphy"

-##' This class stores information of HYPHY output

-##'

-##'

-##' @name hyphy-class

-##' @docType class

-##' @slot fields available features

-##' @slot treetext tree text

-##' @slot phylo phylo object

-##' @slot seq_type one of "NT" and "AA"

-##' @slot subs sequence substitutions

-##' @slot AA_subs Amino acid sequence substitution

-##' @slot ancseq ancestral sequences

-##' @slot tip_seq tip sequences

-##' @slot tip.fasfile fasta file of tip sequences

-##' @slot tree.file tree file

-##' @slot ancseq.file ancestral sequence file, nexus format

-##' @slot extraInfo extra information

-##' @exportClass hyphy

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @seealso \linkS4class{paml_rst}

-##' @keywords classes

-setClass("hyphy",

-         representation  = representation(

-             fields      = "character",

-             treetext    = "character",

-             phylo       = "phylo",

-             seq_type    = "character",

-             subs        = "data.frame",

-             AA_subs     = "data.frame",

-             ancseq      = "character",

-             tip_seq     = "character",

-             tip.fasfile = "character",

-             tree.file   = "character",

-             ancseq.file = "character",

-             extraInfo   = "data.frame"

-             )

-         )

-##' Class "r8s"

-##' This class stores output info from r8s

-##'

-##'

-##' @name r8s-class

-##' @docType class

-##' @slot file input file

-##' @slot fields available feature

-##' @slot treetext tree text

-##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree

-##' @slot extraInfo extra information

-##' @exportClass r8s

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @keywords classes

-setClass("r8s",

-         representation = representation(

-             file      = "character",

-             fields    = "character",

-             treetext  = "character",

-             phylo     = "multiPhylo",

-             extraInfo = "data.frame"

-             )

-         )

-##' Class "nhx"

-##' This class stores nhx tree

-##'

-##'

-##' @name nhx-class

-##' @rdname nhx-class

-##' @docType class

-##' @slot file input file

-##' @slot fields available feature

-##' @slot phylo phylo object

-##' @slot nhx_tags tag information in nhx file

-##' @slot extraInfo extra information

-##' @exportClass nhx

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @keywords classes

-setClass("nhx",

-         representation = representation(

-             file = "character",

-             fields = "character",

-             phylo = "phylo",

-             nhx_tags = "data.frame",

-             extraInfo = "data.frame"

-         )

-         )

+supported_tree_object <- function() {

+    c("apeBootstrap",

+      "beast",

+      "codeml_mlc",

+      "codeml",

+      "hyphy",

+      "jplace",

+      "nhx",

+      "paml_rst",

+      "phangorn",      

+      "phylip",

+      "r8s",

+      "raxml")

+}

 ##' Class "apeBootstrap"

 ##' This class stores ape bootstrapping analysis result

@@ -107,7 +32,7 @@ setClass("nhx",

 ##' @slot bootstrap bootstrap value

 ##' @slot extraInfo extra information

 ##' @exportClass apeBootstrap

-##' @author Guangchuang Yu \url{http://ygc.name}

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

 ##' @keywords classes

 setClass("apeBootstrap",

          representation = representation(

@@ -118,31 +43,69 @@ setClass("apeBootstrap",

          )

          )

+##' Class "beast"

+##' This class stores information of beast output

+##'

+##'

+##' @name beast-class

+##' @aliases beast-class

+##'      get.tree,beast-method

+##' 

+##' @docType class

+##' @slot fields beast statistic variables

+##' @slot treetext tree text in beast file

+##' @slot phylo tree phylo object

+##' @slot translation tip number to name translation in beast file

+##' @slot stats beast statistics

+##' @slot file beast file, nexus format

+##' @slot extraInfo extra information

+##' @exportClass beast

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @seealso \code{\link{show}} \code{\link{get.fields}}

+##'           \code{\link{ggtree}}

+##' @keywords classes

+setClass("beast",

+         representation  = representation(

+             fields      = "character",

+             treetext    = "character",

+             phylo       = "phylo",

+             translation = "matrix",

+             stats       = "data.frame",

+             file        = "character",

+             extraInfo   = "data.frame"

+             )

+         )

+

-##' Class "raxml"

-##' This class stores RAxML bootstrapping analysis result

+##' Class "codeml_mlc"

+##' This class stores information of mlc file frm codeml output

 ##'

 ##'

-##' @name raxml-class

+##' @name codeml_mlc-class

 ##' @docType class

-##' @slot file input file

 ##' @slot fields available features

 ##' @slot treetext tree text

-##' @slot phylo phylo object of treetext

-##' @slot bootstrap bootstrap value

+##' @slot phylo phylo object

+##' @slot dNdS dN dS information

+##' @slot mlcfile mlc file

 ##' @slot extraInfo extra information

-##' @exportClass raxml

-##' @author Guangchuang Yu \url{http://ygc.name}

+##' @exportClass codeml_mlc

+##' @author Guangchuang Yu

+##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}

 ##' @keywords classes

-setClass("raxml",

+setClass("codeml_mlc",

          representation = representation(

-             file       = "character",

-             treetext   = "character"

-         ),

-         contains = "apeBootstrap"

+             fields     = "character",

+             treetext   = "character",

+             phylo      = "phylo",

+             dNdS       = "matrix",

+             ## seq_type   = "character",

+             ## tip_seq    = "character",

+             mlcfile    = "character",

+             extraInfo  = "data.frame"

+             )

          )

-

 ##' Class "paml_rst"

 ##' This class stores information of rst file from PAML output

 ##'

@@ -167,7 +130,7 @@ setClass("raxml",

 ##' @slot rstfile rst file

 ##' @slot extraInfo extra information

 ##' @exportClass paml_rst

-##' @author Guangchuang Yu \url{http://ygc.name}

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

 ##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}

 ##' @keywords classes

 setClass("paml_rst",

@@ -188,66 +151,6 @@ setClass("paml_rst",

          )

          )

-##' Class "phangorn"

-##' This class stores ancestral sequences inferred from 'phangorn'

-##'

-##'

-##' @name phangorn-class

-##' @docType class

-##' @slot fields available attributes

-##' @slot phylo phylo object

-##' @slot seq_type one of "NT" and "AA"

-##' @slot tip_seq sequences of tips

-##' @slot ancseq ancenstral sequences

-##' @slot subs sequence substitution

-##' @slot AA_subs Amino acid sequence substitution

-##' @slot extraInfo extra information

-##' @exportClass phangorn

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @seealso \linkS4class{paml_rst}

-##' @keywords classes

-setClass("phangorn",

-         representation = representation(

-             fields = "character",

-             phylo = "phylo",

-             seq_type = "character",

-             tip_seq = "character",

-             ancseq = "character",

-             subs = "data.frame",

-             AA_subs = "data.frame",

-             extraInfo = "data.frame")

-         )

-

-

-##' Class "codeml_mlc"

-##' This class stores information of mlc file frm codeml output

-##'

-##'

-##' @name codeml_mlc-class

-##' @docType class

-##' @slot fields available features

-##' @slot treetext tree text

-##' @slot phylo phylo object

-##' @slot dNdS dN dS information

-##' @slot mlcfile mlc file

-##' @slot extraInfo extra information

-##' @exportClass codeml_mlc

-##' @author Guangchuang Yu

-##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}

-##' @keywords classes

-setClass("codeml_mlc",

-         representation = representation(

-             fields     = "character",

-             treetext   = "character",

-             phylo      = "phylo",

-             dNdS       = "matrix",

-             ## seq_type   = "character",

-             ## tip_seq    = "character",

-             mlcfile    = "character",

-             extraInfo  = "data.frame"

-             )

-         )

-

 ##' Class "codeml"

 ##' This class stores information of output from codeml

 ##'

@@ -268,6 +171,47 @@ setClass("codeml",

              )

          )

+

+

+##' Class "hyphy"

+##' This class stores information of HYPHY output

+##'

+##'

+##' @name hyphy-class

+##' @docType class

+##' @slot fields available features

+##' @slot treetext tree text

+##' @slot phylo phylo object

+##' @slot seq_type one of "NT" and "AA"

+##' @slot subs sequence substitutions

+##' @slot AA_subs Amino acid sequence substitution

+##' @slot ancseq ancestral sequences

+##' @slot tip_seq tip sequences

+##' @slot tip.fasfile fasta file of tip sequences

+##' @slot tree.file tree file

+##' @slot ancseq.file ancestral sequence file, nexus format

+##' @slot extraInfo extra information

+##' @exportClass hyphy

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @seealso \linkS4class{paml_rst}

+##' @keywords classes

+setClass("hyphy",

+         representation  = representation(

+             fields      = "character",

+             treetext    = "character",

+             phylo       = "phylo",

+             seq_type    = "character",

+             subs        = "data.frame",

+             AA_subs     = "data.frame",

+             ancseq      = "character",

+             tip_seq     = "character",

+             tip.fasfile = "character",

+             tree.file   = "character",

+             ancseq.file = "character",

+             extraInfo   = "data.frame"

+             )

+         )

+

 ##' Class "jplace"

 ##' This class stores information of jplace file.

 ##'

@@ -290,7 +234,7 @@ setClass("codeml",

 ##' @slot file jplace file

 ##' @slot extraInfo extra information

 ##' @exportClass jplace

-##' @author Guangchuang Yu \url{http://ygc.name}

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

 ##' @seealso \code{\link{show}} \code{\link{get.tree}}

 ##'          \code{\link{ggtree}}

 ##' @keywords classes

@@ -307,35 +251,136 @@ setClass("jplace",

              )

          )

-##' Class "beast"

-##' This class stores information of beast output

+

+##' Class "nhx"

+##' This class stores nhx tree

 ##'

 ##'

-##' @name beast-class

-##' @aliases beast-class

-##'      get.tree,beast-method

-##' 

+##' @name nhx-class

+##' @rdname nhx-class

 ##' @docType class

-##' @slot fields beast statistic variables

-##' @slot treetext tree text in beast file

-##' @slot phylo tree phylo object

-##' @slot translation tip number to name translation in beast file

-##' @slot stats beast statistics

-##' @slot file beast file, nexus format

+##' @slot file input file

+##' @slot fields available feature

+##' @slot phylo phylo object

+##' @slot nhx_tags tag information in nhx file

 ##' @slot extraInfo extra information

-##' @exportClass beast

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @seealso \code{\link{show}} \code{\link{get.fields}}

-##'           \code{\link{ggtree}}

+##' @exportClass nhx

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

 ##' @keywords classes

-setClass("beast",

-         representation  = representation(

-             fields      = "character",

-             treetext    = "character",

-             phylo       = "phylo",

-             translation = "matrix",

-             stats       = "data.frame",

-             file        = "character",

-             extraInfo   = "data.frame"

+setClass("nhx",

+         representation = representation(

+             file = "character",

+             fields = "character",

+             phylo = "phylo",

+             nhx_tags = "data.frame",

+             extraInfo = "data.frame"

+         )

+         )

+

+

+##' Class "phangorn"

+##' This class stores ancestral sequences inferred from 'phangorn'

+##'

+##'

+##' @name phangorn-class

+##' @docType class

+##' @slot fields available attributes

+##' @slot phylo phylo object

+##' @slot seq_type one of "NT" and "AA"

+##' @slot tip_seq sequences of tips

+##' @slot ancseq ancenstral sequences

+##' @slot subs sequence substitution

+##' @slot AA_subs Amino acid sequence substitution

+##' @slot extraInfo extra information

+##' @exportClass phangorn

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @seealso \linkS4class{paml_rst}

+##' @keywords classes

+setClass("phangorn",

+         representation = representation(

+             fields = "character",

+             phylo = "phylo",

+             seq_type = "character",

+             tip_seq = "character",

+             ancseq = "character",

+             subs = "data.frame",

+             AA_subs = "data.frame",

+             extraInfo = "data.frame")

+         )

+

+

+##' Class "phylip"

+##' This class stores phylip tree(s)

+##'

+##'

+##' @name phylip-class

+##' @docType class

+##' @slot file input file

+##' @slot fields available feature

+##' @slot phylo phylo or multiPhylo

+##' @slot ntree number of trees

+##' @slot sequence sequences

+##' @slot extraInfo extra information

+##' @exportClass phylip

+##' @author Guangchuang Yu

+##' @keywords classes

+setClass("phylip",

+         representation = representation(

+             file = "character",

+             fields = "character",

+             phylo = "phyloOrmultiPhylo",

+             ntree = "numeric",

+             sequence = "BStringSet",

+             extraInfo = "data.frame")

+         )

+

+

+##' Class "r8s"

+##' This class stores output info from r8s

+##'

+##'

+##' @name r8s-class

+##' @docType class

+##' @slot file input file

+##' @slot fields available feature

+##' @slot treetext tree text

+##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree

+##' @slot extraInfo extra information

+##' @exportClass r8s

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @keywords classes

+setClass("r8s",

+         representation = representation(

+             file      = "character",

+             fields    = "character",

+             treetext  = "character",

+             phylo     = "multiPhylo",

+             extraInfo = "data.frame"

              )

          )

+

+

+##' Class "raxml"

+##' This class stores RAxML bootstrapping analysis result

+##'

+##'

+##' @name raxml-class

+##' @docType class

+##' @slot file input file

+##' @slot fields available features

+##' @slot treetext tree text

+##' @slot phylo phylo object of treetext

+##' @slot bootstrap bootstrap value

+##' @slot extraInfo extra information

+##' @exportClass raxml

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @keywords classes

+setClass("raxml",

+         representation = representation(

+             file       = "character",

+             treetext   = "character"

+         ),

+         contains = "apeBootstrap"

+         )

+

+

@@ -7,7 +7,7 @@

 ##' @export

 ##' @author Guangchuang Yu

 Date2decimal <- function(x) {

-    x %<>% as.Date

+    x <- as.Date(x)

     year <- format(x, "%Y")

     y <- x - as.Date(paste0(year, "-01-01"))

     as.numeric(year) + as.numeric(y)/365

@@ -86,14 +86,6 @@ get_nhx_feature_internal <- function(feature, nameSET) {

 }

-##' @rdname get.tree-methods

-##' @exportMethod get.tree

-setMethod("get.tree", signature(object = "nhx"),

-          function(object) {

-              object@phylo

-          }

-          )

-

@@ -12,7 +12,7 @@ read.raxml <- function(file) {

     phylo <- read.tree(text=tree_text)

     if(any(grepl('@', phylo$node.label))) {

         bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))

-        phylo$node.label %<>% gsub("@\\d+", "", .)

+        phylo$node.label <- gsub("@\\d+", "", phylo$node.label)

     }

     if (all(phylo$node.label == "")) {

@@ -92,17 +92,6 @@ setMethod("scale_color", signature(object="apeBootstrap"),

           })

-

-

-##' @rdname get.tree-methods

-##' @exportMethod get.tree

-setMethod("get.tree", signature(object="apeBootstrap"),

-          function(object,...) {

-              object@phylo

-          }

-          )

-

-

 ##' @rdname get.fields-methods

 ##' @exportMethod get.fields

 setMethod("get.fields", signature(object="apeBootstrap"),

@@ -38,32 +38,6 @@ read.beast <- function(file) {

-##' @rdname groupClade-methods

-##' @exportMethod groupClade

-setMethod("groupClade", signature(object="beast"),

-          function(object, node, group_name="group") {

-              groupClade_(object, node, group_name)

-          })

-

-

-

-##' get.tree method

-##'

-##'

-##' @docType methods

-##' @name get.tree

-##' @rdname get.tree-methods

-##' @aliases get.tree,beast

-##' @exportMethod get.tree

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @usage get.tree(object, ...)

-setMethod("get.tree", signature(object="beast"),

-          function(object,...) {

-              object@phylo

-          }

-          )

-

-

 ##' @rdname get.fields-methods

 ##' @exportMethod get.fields

 setMethod("get.fields", signature(object="beast"),

@@ -22,13 +22,6 @@ read.codeml <- function(rstfile, mlcfile) {

 }

-##' @rdname groupClade-methods

-##' @exportMethod groupClade

-setMethod("groupClade", signature(object="codeml"),

-          function(object, node, group_name="group") {

-              groupClade_(object, node, group_name)

-          }

-          )

 ##' @rdname scale_color-methods

@@ -40,19 +33,6 @@ setMethod("scale_color", signature(object="codeml"),

-##' @rdname show-methods

-##' @exportMethod show

-setMethod("show", signature(object = "codeml"),

-          function(object) {

-              cat("'codeml' S4 object that stored information of\n\t",

-                  paste0("'", object@rst@rstfile, "' and \n\t'",

-                         object@mlc@mlcfile, "'."),

-                  "\n\n")

-              cat("...@ tree:")

-              print.phylo(get.tree(object))                  

-              cat("\nwith the following features available:\n")

-              print_fields(object, len=4)

-          })

 ##' @rdname get.tipseq-methods

 ##' @exportMethod get.tipseq

@@ -61,17 +41,6 @@ setMethod("get.tipseq", signature(object = "codeml"),

               return(object@rst@tip_seq)

           })

-##' @rdname get.tree-methods

-##' @exportMethod get.tree

-##' @param by one of rst or mlc

-setMethod("get.tree", signature(object="codeml"),

-          function(object, by="rst", ...) {

-              if (by == "rst") {

-                  return(object@rst@phylo)

-              } else {

-                  return(object@mlc@phylo)

-              }

-          })

 ##' @rdname get.subs-methods

 ##' @exportMethod get.subs

@@ -133,7 +133,25 @@ get_heatmap_column_position <- function(treeview, by="bottom") {

 ##' @importFrom ggplot2 scale_fill_manual

 ##' @author Guangchuang Yu

 msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

-    aln <- readBStringSet(fasta)

+    if (missingArg(fasta)) {

+        aln <- NULL

+    } else if (is(fasta, "BStringSet")) {

+        aln <- fasta

+    } else if (is(fasta, "character")) {

+        aln <- readBStringSet(fasta)

+    } else {

+        aln <- NULL

+    }

+        

+    if (is(p, "phylip")) {

+        aln <- p@sequence

+        p <- ggtree(p) + geom_tiplab()

+    }

+

+    if (is.null(aln)) {

+        stop("multiple sequence alignment is not available...\n-> check the parameter 'fasta'...")

+    }

+    

     if (is.null(window)) {

         window <- c(1, width(aln)[1])

     }

@@ -26,21 +26,6 @@ read.jplace <- function(file) {

          )

 }

-##' @rdname groupOTU-methods

-##' @exportMethod groupOTU

-setMethod("groupOTU", signature(object="jplace"),

-          function(object, focus, group_name="group") {

-              groupOTU_(object, focus, group_name)

-          }

-          )

-

-##' @rdname groupClade-methods

-##' @exportMethod groupClade

-setMethod("groupClade", signature(object="jplace"),

-          function(object, node, group_name="group") {

-              groupClade_(object, node, group_name)

-          }

-          )

 ##' @rdname scale_color-methods

@@ -51,53 +36,7 @@ setMethod("scale_color", signature(object="jplace"),

           })

-##' @rdname get.tree-methods

-##' @exportMethod get.tree

-setMethod("get.tree", signature(object="jplace"),

-          function(object) {

-              object@phylo

-          })

-

-

-##' show method for \code{jplace} instance

-##'

-##' 

-##' @name show

-##' @docType methods

-##' @rdname show-methods

-##'

-##' @title show method

-##' @param object one of \code{jplace}, \code{beast} object

-##' @return print info

-##' @importFrom methods show

-##' @exportMethod show

-##' @usage show(object)

-##' @author Guangchuang Yu \url{http://ygc.name}

-##' @examples

-##' jp <- system.file("extdata", "sample.jplace", package="ggtree")

-##' jp <- read.jplace(jp)

-##' show(jp)

-setMethod("show", signature(object = "jplace"),

-          function(object) {

-              cat("'jplace' S4 object that stored information of\n\t",

-                  paste0("'", object@file, "'."),

-                  "\n\n")

-

-              cat("...@ tree: ")

-

-              phylo <- get.tree(object)

-              phylo$node.label <- NULL

-              phylo$tip.label %<>% gsub("\\@\\d+", "", .) 

-        

-              print.phylo(phylo)

-              cat("\nwith the following features availables:\n")

-              cat("\t", paste0("'",

-                               paste(get.fields(object), collapse="',\t'"),

-                               "'."),

-                  "\n")

-          }

-          )

 ##' get.treeinfo method

 ##'

@@ -616,6 +616,15 @@ fortify.multiPhylo <-  function(model, data, layout="rectangular",

     return(df)

 }

+##' @method fortify phylip

+##' @export

+fortify.phylip <- function(model, data, layout="rectangular",

+                        ladderize=TRUE, right=FALSE,

+                        branch.length = "TREE", mrsd=NULL, ...) {

+    trees <- get.tree(model)

+    fortify(trees, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)

+}

+    

 ##' @method fortify r8s

 ##' @export

 fortify.r8s <- function(model, data, layout="rectangular",

new file mode 100644

@@ -0,0 +1,61 @@

+##' @rdname get.tree-methods

+##' @exportMethod get.tree

+setMethod("get.tree", signature(object="apeBootstrap"),

+          function(object,...) {

+              object@phylo

+          }

+          )

+

+##' get.tree method

+##'

+##'

+##' @docType methods

+##' @name get.tree

+##' @rdname get.tree-methods

+##' @aliases get.tree,beast

+##' @exportMethod get.tree

+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

+##' @usage get.tree(object, ...)

+setMethod("get.tree", signature(object="beast"),

+          function(object,...) {

+              object@phylo

+          }

+          )

+

+